Correlation between copy number variation genes (focal events) and molecular subtypes

Pheochromocytoma and Paraganglioma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1SF2TZX

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 30 focal events and 8 molecular subtypes across 160 patients, 35 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.3 cnv correlated to 'CN_CNMF'.
amp_14q24.3 cnv correlated to 'CN_CNMF'.
del_1p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p24.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q26.1 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_11p15.4 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q22.1 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_17p13.2 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_17q11.2 cnv correlated to 'CN_CNMF'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 30 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 35 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
del 11p15 4	57 (36%)	103	1e-05 (0.0024)	3e-05 (0.00669)	0.00024 (0.0516)	1e-05 (0.0024)	0.00012 (0.0263)	1e-05 (0.0024)	1e-05 (0.0024)	4e-05 (0.00888)
del 1p12	111 (69%)	49	1e-05 (0.0024)	1e-05 (0.0024)	1e-05 (0.0024)	1e-05 (0.0024)	0.00057 (0.121)	0.0182 (1.00)	0.00036 (0.077)	0.00058 (0.122)
del 3p24 1	60 (38%)	100	1e-05 (0.0024)	0.00323 (0.623)	0.00015 (0.0327)	2e-05 (0.0045)	2e-05 (0.0045)	0.00022 (0.0475)	8e-05 (0.0176)	0.00086 (0.178)
del 22q13 31	64 (40%)	96	1e-05 (0.0024)	0.00962 (1.00)	0.00312 (0.608)	0.00018 (0.0391)	0.00155 (0.316)	0.0073 (1.00)	0.00467 (0.873)	0.0007 (0.146)
del 3q26 1	93 (58%)	67	1e-05 (0.0024)	0.573 (1.00)	0.0199 (1.00)	1e-05 (0.0024)	0.0133 (1.00)	0.006 (1.00)	0.0957 (1.00)	0.00362 (0.688)
del 11q22 1	44 (28%)	116	1e-05 (0.0024)	0.207 (1.00)	0.00294 (0.576)	0.00421 (0.791)	0.00467 (0.873)	0.00103 (0.212)	0.00133 (0.273)	0.00411 (0.777)
del 17p13 2	64 (40%)	96	7e-05 (0.0155)	0.00045 (0.0958)	0.0128 (1.00)	0.0053 (0.975)	0.0241 (1.00)	0.00707 (1.00)	0.00213 (0.43)	0.0194 (1.00)
amp 1q21 3	30 (19%)	130	1e-05 (0.0024)	0.608 (1.00)	0.643 (1.00)	0.958 (1.00)	0.903 (1.00)	0.442 (1.00)	0.254 (1.00)	0.842 (1.00)
amp 14q24 3	10 (6%)	150	0.00076 (0.158)	0.199 (1.00)	0.853 (1.00)	0.169 (1.00)	0.457 (1.00)	0.713 (1.00)	0.0604 (1.00)	0.598 (1.00)
del 17q11 2	42 (26%)	118	1e-05 (0.0024)	0.00335 (0.64)	0.0222 (1.00)	0.00254 (0.505)	0.0924 (1.00)	0.0682 (1.00)	0.00251 (0.502)	0.0321 (1.00)
del xp21 1	46 (29%)	114	0.00263 (0.521)	0.00569 (1.00)	0.0323 (1.00)	0.00313 (0.608)	0.00062 (0.13)	0.0417 (1.00)	0.0495 (1.00)	0.0133 (1.00)
amp 4q25	6 (4%)	154	0.697 (1.00)	0.762 (1.00)	0.133 (1.00)	0.382 (1.00)	0.765 (1.00)	0.63 (1.00)	0.377 (1.00)	0.762 (1.00)
amp 4q31 1	12 (8%)	148	0.0809 (1.00)	0.086 (1.00)	0.749 (1.00)	0.0189 (1.00)	0.199 (1.00)	0.185 (1.00)	0.128 (1.00)	0.747 (1.00)
amp 11p15 2	7 (4%)	153	0.405 (1.00)	0.141 (1.00)	0.0909 (1.00)	0.0924 (1.00)	0.165 (1.00)	0.178 (1.00)	0.0483 (1.00)	0.107 (1.00)
amp 12q13 3	16 (10%)	144	0.079 (1.00)	0.14 (1.00)	0.615 (1.00)	0.621 (1.00)	0.047 (1.00)	0.261 (1.00)	0.00821 (1.00)	0.101 (1.00)
amp 17q21 31	15 (9%)	145	0.122 (1.00)	0.83 (1.00)	0.702 (1.00)	0.00158 (0.321)	0.888 (1.00)	0.2 (1.00)	0.194 (1.00)	0.396 (1.00)
del 1q44	21 (13%)	139	0.0554 (1.00)	0.35 (1.00)	0.0809 (1.00)	0.27 (1.00)	0.381 (1.00)	0.716 (1.00)	0.023 (1.00)	0.185 (1.00)
del 2q34	13 (8%)	147	0.0594 (1.00)	0.447 (1.00)	0.418 (1.00)	0.143 (1.00)	0.532 (1.00)	0.0946 (1.00)	0.617 (1.00)	0.305 (1.00)
del 4q22 1	15 (9%)	145	0.018 (1.00)	0.225 (1.00)	0.00778 (1.00)	0.0793 (1.00)	0.127 (1.00)	0.29 (1.00)	0.122 (1.00)	0.2 (1.00)
del 4q35 2	16 (10%)	144	0.00276 (0.544)	0.521 (1.00)	0.233 (1.00)	0.369 (1.00)	0.752 (1.00)	0.641 (1.00)	0.528 (1.00)	0.53 (1.00)
del 5q15	12 (8%)	148	0.277 (1.00)	1 (1.00)	0.973 (1.00)	1 (1.00)	0.928 (1.00)	0.187 (1.00)	0.866 (1.00)	0.75 (1.00)
del 6p12 3	10 (6%)	150	0.185 (1.00)	0.265 (1.00)	0.0205 (1.00)	0.0926 (1.00)	0.199 (1.00)	0.169 (1.00)	0.767 (1.00)	0.199 (1.00)
del 6q16 1	24 (15%)	136	0.357 (1.00)	0.0742 (1.00)	0.0255 (1.00)	0.00736 (1.00)	0.0167 (1.00)	0.00523 (0.968)	0.00624 (1.00)	0.00329 (0.632)
del 7q33	8 (5%)	152	0.031 (1.00)	0.257 (1.00)	0.00662 (1.00)	0.0505 (1.00)	0.0167 (1.00)	0.00612 (1.00)	0.525 (1.00)	0.00927 (1.00)
del 8p22	24 (15%)	136	0.0605 (1.00)	0.124 (1.00)	0.00247 (0.496)	0.00657 (1.00)	0.152 (1.00)	0.155 (1.00)	0.0251 (1.00)	0.187 (1.00)
del 9p24 2	15 (9%)	145	0.476 (1.00)	0.339 (1.00)	0.0839 (1.00)	0.167 (1.00)	0.514 (1.00)	0.0729 (1.00)	0.351 (1.00)	0.542 (1.00)
del 9q21 12	14 (9%)	146	0.562 (1.00)	0.553 (1.00)	0.362 (1.00)	0.358 (1.00)	0.723 (1.00)	0.116 (1.00)	0.826 (1.00)	1 (1.00)
del 12q21 33	8 (5%)	152	0.323 (1.00)	0.893 (1.00)	0.912 (1.00)	0.876 (1.00)	0.594 (1.00)	0.702 (1.00)	0.409 (1.00)	0.527 (1.00)
del 13q22 3	7 (4%)	153	0.726 (1.00)	0.889 (1.00)	0.368 (1.00)	0.676 (1.00)	0.794 (1.00)	0.451 (1.00)	0.541 (1.00)	0.484 (1.00)
del 16q21	5 (3%)	155	0.0144 (1.00)	0.114 (1.00)	0.554 (1.00)	0.0146 (1.00)	0.212 (1.00)	0.592 (1.00)	0.452 (1.00)	0.851 (1.00)

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S1. Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	24	55	43	23
AMP PEAK 1(1Q21.3) MUTATED	15	3	5	2	5
AMP PEAK 1(1Q21.3) WILD-TYPE	0	21	50	41	18

Figure S1. Get High-res Image Gene #1: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q24.3' versus 'CN_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.16

Table S2. Gene #6: 'amp_14q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	24	55	43	23
AMP PEAK 6(14Q24.3) MUTATED	0	0	1	9	0
AMP PEAK 6(14Q24.3) WILD-TYPE	15	24	54	34	23

Figure S2. Get High-res Image Gene #6: 'amp_14q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S3. Gene #8: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	24	55	43	23
DEL PEAK 1(1P12) MUTATED	14	0	48	27	22
DEL PEAK 1(1P12) WILD-TYPE	1	24	7	16	1

Figure S3. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S4. Gene #8: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	77	43
DEL PEAK 1(1P12) MUTATED	24	67	20
DEL PEAK 1(1P12) WILD-TYPE	16	10	23

Figure S4. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S5. Gene #8: 'del_1p12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	63	43	21
DEL PEAK 1(1P12) MUTATED	24	57	20	10
DEL PEAK 1(1P12) WILD-TYPE	9	6	23	11

Figure S5. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S6. Gene #8: 'del_1p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	63	43	21
DEL PEAK 1(1P12) MUTATED	18	57	27	9
DEL PEAK 1(1P12) WILD-TYPE	15	6	16	12

Figure S6. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p12' versus 'MIRSEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.12

Table S7. Gene #8: 'del_1p12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	57	39
DEL PEAK 1(1P12) MUTATED	38	50	23
DEL PEAK 1(1P12) WILD-TYPE	26	7	16

Figure S7. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.077

Table S8. Gene #8: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	66	57
DEL PEAK 1(1P12) MUTATED	21	57	33
DEL PEAK 1(1P12) WILD-TYPE	16	9	24

Figure S8. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.12

Table S9. Gene #8: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	53	39
DEL PEAK 1(1P12) MUTATED	41	47	23
DEL PEAK 1(1P12) WILD-TYPE	27	6	16

Figure S9. Get High-res Image Gene #8: 'del_1p12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S10. Gene #11: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	24	55	43	23
DEL PEAK 4(3P24.1) MUTATED	9	1	12	32	6
DEL PEAK 4(3P24.1) WILD-TYPE	6	23	43	11	17

Figure S10. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p24.1' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.033

Table S11. Gene #11: 'del_3p24.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	63	43	21
DEL PEAK 4(3P24.1) MUTATED	17	15	25	3
DEL PEAK 4(3P24.1) WILD-TYPE	16	48	18	18

Figure S11. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0045

Table S12. Gene #11: 'del_3p24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	63	43	21
DEL PEAK 4(3P24.1) MUTATED	11	16	30	3
DEL PEAK 4(3P24.1) WILD-TYPE	22	47	13	18

Figure S12. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0045

Table S13. Gene #11: 'del_3p24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	57	39
DEL PEAK 4(3P24.1) MUTATED	37	17	6
DEL PEAK 4(3P24.1) WILD-TYPE	27	40	33

Figure S13. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.048

Table S14. Gene #11: 'del_3p24.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	53	18	24
DEL PEAK 4(3P24.1) MUTATED	37	14	6	3
DEL PEAK 4(3P24.1) WILD-TYPE	28	39	12	21

Figure S14. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.018

Table S15. Gene #11: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	66	57
DEL PEAK 4(3P24.1) MUTATED	25	16	19
DEL PEAK 4(3P24.1) WILD-TYPE	12	50	38

Figure S15. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.18

Table S16. Gene #11: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	53	39
DEL PEAK 4(3P24.1) MUTATED	37	14	9
DEL PEAK 4(3P24.1) WILD-TYPE	31	39	30

Figure S16. Get High-res Image Gene #11: 'del_3p24.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S17. Gene #12: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	24	55	43	23
DEL PEAK 5(3Q26.1) MUTATED	8	0	38	33	14
DEL PEAK 5(3Q26.1) WILD-TYPE	7	24	17	10	9

Figure S17. Get High-res Image Gene #12: 'del_3q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S18. Gene #12: 'del_3q26.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	63	43	21
DEL PEAK 5(3Q26.1) MUTATED	6	47	33	7
DEL PEAK 5(3Q26.1) WILD-TYPE	27	16	10	14

Figure S18. Get High-res Image Gene #12: 'del_3q26.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.4' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S19. Gene #22: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	24	55	43	23
DEL PEAK 15(11P15.4) MUTATED	5	5	0	36	11
DEL PEAK 15(11P15.4) WILD-TYPE	10	19	55	7	12

Figure S19. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.4' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0067

Table S20. Gene #22: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	77	43
DEL PEAK 15(11P15.4) MUTATED	23	14	20
DEL PEAK 15(11P15.4) WILD-TYPE	17	63	23

Figure S20. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.4' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.052

Table S21. Gene #22: 'del_11p15.4' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	63	43	21
DEL PEAK 15(11P15.4) MUTATED	13	12	26	6
DEL PEAK 15(11P15.4) WILD-TYPE	20	51	17	15

Figure S21. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11p15.4' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S22. Gene #22: 'del_11p15.4' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	63	43	21
DEL PEAK 15(11P15.4) MUTATED	11	9	31	6
DEL PEAK 15(11P15.4) WILD-TYPE	22	54	12	15

Figure S22. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.026

Table S23. Gene #22: 'del_11p15.4' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	57	39
DEL PEAK 15(11P15.4) MUTATED	36	11	10
DEL PEAK 15(11P15.4) WILD-TYPE	28	46	29

Figure S23. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_11p15.4' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S24. Gene #22: 'del_11p15.4' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	53	18	24
DEL PEAK 15(11P15.4) MUTATED	39	7	5	6
DEL PEAK 15(11P15.4) WILD-TYPE	26	46	13	18

Figure S24. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.4' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S25. Gene #22: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	66	57
DEL PEAK 15(11P15.4) MUTATED	26	13	18
DEL PEAK 15(11P15.4) WILD-TYPE	11	53	39

Figure S25. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11p15.4' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0089

Table S26. Gene #22: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	53	39
DEL PEAK 15(11P15.4) MUTATED	38	9	10
DEL PEAK 15(11P15.4) WILD-TYPE	30	44	29

Figure S26. Get High-res Image Gene #22: 'del_11p15.4' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S27. Gene #23: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	24	55	43	23
DEL PEAK 16(11Q22.1) MUTATED	3	3	3	33	2
DEL PEAK 16(11Q22.1) WILD-TYPE	12	21	52	10	21

Figure S27. Get High-res Image Gene #23: 'del_11q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.21

Table S28. Gene #23: 'del_11q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	65	53	18	24
DEL PEAK 16(11Q22.1) MUTATED	28	7	2	7
DEL PEAK 16(11Q22.1) WILD-TYPE	37	46	16	17

Figure S28. Get High-res Image Gene #23: 'del_11q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.015

Table S29. Gene #27: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	24	55	43	23
DEL PEAK 20(17P13.2) MUTATED	5	4	31	22	2
DEL PEAK 20(17P13.2) WILD-TYPE	10	20	24	21	21

Figure S29. Get High-res Image Gene #27: 'del_17p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.2' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.096

Table S30. Gene #27: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	77	43
DEL PEAK 20(17P13.2) MUTATED	9	43	12
DEL PEAK 20(17P13.2) WILD-TYPE	31	34	31

Figure S30. Get High-res Image Gene #27: 'del_17p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S31. Gene #28: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	24	55	43	23
DEL PEAK 21(17Q11.2) MUTATED	1	0	25	16	0
DEL PEAK 21(17Q11.2) WILD-TYPE	14	24	30	27	23

Figure S31. Get High-res Image Gene #28: 'del_17q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0024

Table S32. Gene #29: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	15	24	55	43	23
DEL PEAK 22(22Q13.31) MUTATED	6	6	39	11	2
DEL PEAK 22(22Q13.31) WILD-TYPE	9	18	16	32	21

Figure S32. Get High-res Image Gene #29: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.039

Table S33. Gene #29: 'del_22q13.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	63	43	21
DEL PEAK 22(22Q13.31) MUTATED	13	37	7	7
DEL PEAK 22(22Q13.31) WILD-TYPE	20	26	36	14

Figure S33. Get High-res Image Gene #29: 'del_22q13.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.15

Table S34. Gene #29: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	68	53	39
DEL PEAK 22(22Q13.31) MUTATED	16	30	18
DEL PEAK 22(22Q13.31) WILD-TYPE	52	23	21

Figure S34. Get High-res Image Gene #29: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.13

Table S35. Gene #30: 'del_xp21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	64	57	39
DEL PEAK 23(XP21.1) MUTATED	13	27	6
DEL PEAK 23(XP21.1) WILD-TYPE	51	30	33

Figure S35. Get High-res Image Gene #30: 'del_xp21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = PCPG-TP.transferedmergedcluster.txt
Number of patients = 160
Number of significantly focal cnvs = 30
Number of molecular subtypes = 8
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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